https://github.com/mvinyard/cell-neighbors
Neighbor graphs for single-cell data (AnnData)
https://github.com/mvinyard/cell-neighbors
anndata neighbor-graphs single-cell
Last synced: 3 months ago
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Neighbor graphs for single-cell data (AnnData)
- Host: GitHub
- URL: https://github.com/mvinyard/cell-neighbors
- Owner: mvinyard
- Created: 2024-02-20T20:39:22.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-02-23T14:59:34.000Z (over 1 year ago)
- Last Synced: 2025-02-01T03:37:14.696Z (9 months ago)
- Topics: anndata, neighbor-graphs, single-cell
- Language: Python
- Homepage:
- Size: 399 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# cell-neighbors
Neighbor graphs for single-cell data (AnnData)
This repository provides a Python package for building k-nearest neighbor (kNN) graphs from AnnData objects.
The package is built on the `Annoy` library from Spotify.
## Features
- Efficient kNN Graph Construction from `Annoy`.
- Direct `AnnData` integration
- Flexible querying of neighbors in the constructed `kNN` graph index.
## Installation
You can install the package using pip:
```
pip install cell-neighbors
```
## Example
```python
import cell_neighbors
# Initialize kNN graph builder
knn_graph = cell_neighbors.kNN(adata), use_key="X_pca")
# Query neighbors
X_query = [...] # Your query points as numpy array
neighbors = knn_graph.query(X_query)
```
## Documentation
For real examples, detailed usage instructions, and API reference, please refer to the documentation.